Estimating the accuracy of calculated electron paramagnetic resonance hyperfine couplings for a lytic polysaccharide monooxygenase
(2021) In Computational and Structural Biotechnology Journal 19. p.555-567- Abstract
Lytic polysaccharide monooxygenases (LPMOs) are enzymes that bind polysaccharides followed by an (oxidative) disruption of the polysaccharide surface, thereby boosting depolymerization. The binding process between the LPMO catalytic domain and polysaccharide is key to the mechanism and establishing structure-function relationships for this binding is therefore crucial. The hyperfine coupling constants (HFCs) from EPR spectroscopy have proven useful for this purpose. Unfortunately, EPR does not provide direct structural data and therefore the experimental EPR parameters have to be supported with parameters calculated with density functional theory. Yet, calculated HFCs are extremely sensitive to the employed computational setup. Using... (More)
Lytic polysaccharide monooxygenases (LPMOs) are enzymes that bind polysaccharides followed by an (oxidative) disruption of the polysaccharide surface, thereby boosting depolymerization. The binding process between the LPMO catalytic domain and polysaccharide is key to the mechanism and establishing structure-function relationships for this binding is therefore crucial. The hyperfine coupling constants (HFCs) from EPR spectroscopy have proven useful for this purpose. Unfortunately, EPR does not provide direct structural data and therefore the experimental EPR parameters have to be supported with parameters calculated with density functional theory. Yet, calculated HFCs are extremely sensitive to the employed computational setup. Using the LPMO Ls(AA9)A catalytic domain, we here quantify the importance of several choices in the computational setup, ranging from the use of specialized basis, the underlying structures, and the employed exchange-correlation functional. We show that specialized basis sets are an absolute necessity, and also that care has to be taken in the optimization of the underlying structure: only by allowing large parts of the protein around the active site to structurally relax could we obtain results that uniformly reproduced experimental trends. We compare our results to previously published X-ray structures and experimental HFCs for Ls(AA9)A as well as to recent experimental/theoretical results for another (AA10) family of LPMOs.
(Less)
- author
- Theibich, Yusuf A. ; Sauer, Stephan P.A. ; Leggio, Leila Lo and Hedegård, Erik D. LU
- organization
- publishing date
- 2021
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- DFT, EPR, LPMO, QM/MM
- in
- Computational and Structural Biotechnology Journal
- volume
- 19
- pages
- 13 pages
- publisher
- Research Network of Computational and Structural Biotechnology
- external identifiers
-
- scopus:85099173426
- pmid:33510861
- ISSN
- 2001-0370
- DOI
- 10.1016/j.csbj.2020.12.014
- language
- English
- LU publication?
- yes
- id
- 6738e2f7-5e33-42ab-8b9a-76fd39421e71
- date added to LUP
- 2021-01-25 11:38:42
- date last changed
- 2024-06-27 07:39:24
@article{6738e2f7-5e33-42ab-8b9a-76fd39421e71,
abstract = {{<p>Lytic polysaccharide monooxygenases (LPMOs) are enzymes that bind polysaccharides followed by an (oxidative) disruption of the polysaccharide surface, thereby boosting depolymerization. The binding process between the LPMO catalytic domain and polysaccharide is key to the mechanism and establishing structure-function relationships for this binding is therefore crucial. The hyperfine coupling constants (HFCs) from EPR spectroscopy have proven useful for this purpose. Unfortunately, EPR does not provide direct structural data and therefore the experimental EPR parameters have to be supported with parameters calculated with density functional theory. Yet, calculated HFCs are extremely sensitive to the employed computational setup. Using the LPMO Ls(AA9)A catalytic domain, we here quantify the importance of several choices in the computational setup, ranging from the use of specialized basis, the underlying structures, and the employed exchange-correlation functional. We show that specialized basis sets are an absolute necessity, and also that care has to be taken in the optimization of the underlying structure: only by allowing large parts of the protein around the active site to structurally relax could we obtain results that uniformly reproduced experimental trends. We compare our results to previously published X-ray structures and experimental HFCs for Ls(AA9)A as well as to recent experimental/theoretical results for another (AA10) family of LPMOs.</p>}},
author = {{Theibich, Yusuf A. and Sauer, Stephan P.A. and Leggio, Leila Lo and Hedegård, Erik D.}},
issn = {{2001-0370}},
keywords = {{DFT; EPR; LPMO; QM/MM}},
language = {{eng}},
pages = {{555--567}},
publisher = {{Research Network of Computational and Structural Biotechnology}},
series = {{Computational and Structural Biotechnology Journal}},
title = {{Estimating the accuracy of calculated electron paramagnetic resonance hyperfine couplings for a lytic polysaccharide monooxygenase}},
url = {{http://dx.doi.org/10.1016/j.csbj.2020.12.014}},
doi = {{10.1016/j.csbj.2020.12.014}},
volume = {{19}},
year = {{2021}},
}